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Briefings in Functional Genomics and Proteomics Advance Access published online on May 29, 2008
Briefings in Functional Genomics and Proteomics, doi:10.1093/bfgp/eln023
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© The Author 2008. Published by Oxford University Press. For permissions, please email: journals.permissions@oxfordjournals.org

The untiring search for the most complete proteome representation: reviewing the methods

Daniel Martins de Souza, Bruno M. Oliveira, Erich Castro-Dias, Flavia V. Winck, Ricardo S. O. Horiuchi, Paulo A. Baldasso, Hugo T. Caetano, Natália Katauchi Dayane Pires, Sergio Marangoni and José C. Novello

Corresponding author. Daniel Martins de Souza, Laboratório de Proteômica, Departamento de Bioquímica, Instituto de Biologia, UNICAMP - Campinas, SP 13083-970, Brazil. Tel/Fax: 55-19-35216654, E-mail: java99{at}unicamp.br

Proteomic research has proved valuable for understanding the molecular mechanisms of biological processes, as well as in the search for biomarkers for a variety of diseases which lack a molecular diagnostic. While several new approaches are being developed, two-dimensional (2-DE) gel electrophoresis is still one of the most commonly used techniques, despite its many limitations. However, for biomarker research, 2-DE gel electrophoresis alone does not fulfill the necessary pre-requisites. If such a technique is utilized exclusively, a great part of a given proteome remains unseen. Therefore, very precise and sensitive techniques are needed. Here, we present a brief review of known methodologies that try to overcome the limitations of conventional proteome analysis as well as their respective advantages and limitations.

Keywords: two-dimensional gel electrophoresis, 2D, 2DE, 2-DE, proteome, proteomics, shotgun, narrow-range, NEPHGE, pre-fractionation, HPLC, depletion, DIGE, protein arrays, low-expressed proteins, high-expressed proteins


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